Suite of data science tools build by Fraunhofer ITMP

• Owner: Yojana Gadiya

**SNRApp** is an interactive web app to calculate the Signal-to-Noise Ratio (SNR) from spatial omics data. The user will need to upload an `anndata` and set the top and bottom percentile.

• Owner: Nima Rafati

Test suite

• Owner: Yojana Gadiya

This app provides a reference database of proteins found in dried blood spots, based on published scientific studies. It serves as a tool for exploring the dried blood spot proteome.

• Owner: William Stauch

starbase is a database and toolkit for exploring of large transposable elements in Fungi

• Owner: Adrian Forsythe

TurgoLab is an interactive, FEM-based simulation app for inflating 2D cellular structures from .geo files. It integrates the BVPy framework to enable intuitive biomechanical modeling of plant tissues under turgor pressure from the geometry made with Anatomeshr .

• Owner: Adrien Heymans

TissUUmaps demo

• Owner: Christophe Avenel

• Owner: Isabelle Leo

A converter of 2D plant anatomical data into finite element mesh (GEO) format.

• Owner: Adrien Heymans

A shiny application to process OLINK data. Outlier detection - filtering - statistical analysis - visualization - publication ready figures all at one place.

• Owner: Debojyoti Das

Visualizations of the results from an interaction screen of 215 G protein-coupled receptors (GPCRs) and the receptor activity–modifying proteins (RAMPs). Companion app to ‘Multiplexed mapping of the interactome of GPCRs with receptor activity–modifying proteins’, https://doi.org/10.1126/sciadv.ado9959

• Owner: Leo Dahl

This site provides a databases of knockout designs targeting the entire Plasmodium berghei protein encoding genome using the PbHiT CRISPR system as described in Jonsdottir et al. DOI: https://doi.org/10.1101/2024.04.20.590404

• Owner: Johan Henriksson

Visualizations of the results from a selectivity screen of >400 antibodies targeting 215 G protein-coupled receptors (GPCRs). Companion app to ‘Multiplexed selectivity screening of anti-GPCR antibodies’, https://doi.org/10.1126/sciadv.adf9297

• Owner: Leo Dahl

ShinyCell app detailing cellular landscape of equine asthma

• Owner: Amanda Raine

Biome-specific gene catalogues have been recovered for many environments using shotgun metagenomics, followed by assembly and gene calling on the assembled contigs. We recently proposed a novel mix-assembly strategy, combining individual and co-assembly approaches, and used this approach to assemble an extensive non-redundant gene set from 124 Bal...tic Sea metagenome samples. The Baltic Sea Gene Set (BAGS v1.1) comprises 66.53 million functionally and taxonomically annotated genes. To enable interactive exploration of this gene catalogue we have developed an RShiny application, BAGS-Shiny, that allows users to perform searches by sequence similarity (BLAST) and/or taxonomic and functional annotation. The gene catalogue and web application will serve as valuable tools for exploring microbial gene functions in brackish ecosystems. [see more]

• Owner: Johan Alfredéen

This Shiny app provides a user-friendly interface for performing quick analysis of Olink data using OlinkAnalyze package. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs.

• Owner: Jyotirmoy Das

KISSE is a species search engine that utilizes collagen sequences from eight different species to identify unknown samples.

• Owner: Hassan Gharibi

Hosting page for AntiMicRobial KG and prediction models.

• Owner: Yojana Gadiya

A Shiny App to Explore Omics Data of Triple Negative Breast Carcinoma

• Owner: Luay Aswad

Supplementary material to Sdougkou et al. 2024, "Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood" Environmental Science & Technology, 58 (37) 16302–16315 https://doi.org/10.1021/acs.est.4c05235

• Owner: Stefano Papazian

Related publication: Li, Xiaofei, et al. "Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin." Nature neuroscience 26.5 (2023): 891-901. https://doi.org/10.1038/s41593-023-01312-9

• Owner: Christophe Avenel

Related publication: Kukanja, Petra, et al. "Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology." Cell 187.8 (2024): 1990-2009. https://doi.org/10.1016/j.cell.2024.02.030

• Owner: Christophe Avenel

Related publication: Andersson, Axel, et al. "Points2Regions: Fast, interactive clustering of imaging‐based spatial transcriptomics data." Cytometry Part A 105.9 (2024): 677-687. https://doi.org/10.1002/cyto.a.24884

• Owner: Christophe Avenel

Related publication: Andersson, Axel, et al. "Cell segmentation of in situ transcriptomics data using signed graph partitioning." International Workshop on Graph-Based Representations in Pattern Recognition. Cham: Springer Nature Switzerland, 2023. https://doi.org/10.1007/978-3-031-42795-4_13

• Owner: Christophe Avenel

Related publication: Ström, Peter, et al. "Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study." The Lancet Oncology 21.2 (2020): 222-232, https://doi.org/10.1016/S1470-2045(19)30738-7/

• Owner: Christophe Avenel

DILI Predictor is an open-source app framework built specifically for human drug-induced liver injury (DILI). DILI Predictor employs eleven proxy-DILI labels from in vitro and in vivo datasets along with pharmacokinetic parameters, structural fingerprints and physicochemical parameters as features.

• Owner: Hamza Saeed

DICTrank Predictor is an open-source app framework built specifically for human drug-induced cardiotoxicity (DICT).DICTrank Predictor employs physicochemical parameters as feature. For more details look at https://www.biorxiv.org/content/10.1101/2023.10.15.562398v1

• Owner: Hamza Saeed

Dashboard for the R4A Expertise KG

• Owner: Yojana Gadiya

Explores interpretability for chest X-ray pathology predictions using methods—Grad-CAM, LIME, SHAP, and LRP. It provides heatmaps and evaluation metrics for better insights into the medical significance of predictions made by deep learning models.

• Owner: Mahbub Ul Alam

enrichedmassspec - a shiny app to visualize differentially expressed proteins (DEPs) and carry out enrichment analysis using different methods on Mass Spectrometry data from generated using spectronaut

• Owner: Debojyoti Das

This is for exploring blood phenotypes in plasmogem screen data.

• Owner: Vikash Pandey

This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs.

• Owner: Jyotirmoy Das

MMAtt-DTA: MultiModal Attention Drug-Target Affinity prediction

• Owner: Aleksandr Kushnir

Demo of Bayesian updating for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesupdate

• Owner: Johan Henriksson

Data exploration analysis tool. Load your csv data file and it will help to clean the data, report the missing/NA values (using pareto graph), perform a set of various statistical analyses (e.g., correlation, t-test, MW-test, KS-test, and more) resulting in tables and graphs.

• Owner: Ilona Szczot

Dashboard plotting the number of people in Sweden aged 0-19 who have have filled a prescription for ADHD medications each year.

• Owner: Arnold Kochari

PK Predictor is an open-source app framework built specifically for predicting human and animal PK parameters

• Owner: Hamza Saeed

Clusetering of phenotype data

• Owner: Vikash Pandey

Comparing 4 types of the most common reference populations for child sex- and age-adjusted Body Mass Index (BMI)

• Owner: Maja Engsner

Service that provides a REST Api to convert between different chemical notations. More info: https://github.com/DouglasConnect/ChemIdConvert.

• Owner: Hamza Saeed

New interventions to control malaria depend on a deep understanding of the parasite that causes the disease. The PlasmoGEM project produces free genetic tools for research on malaria parasites. We also use the reagents in genetic screens to identify parasite gene functions at scale. The purpose of this database is to share data generated by the p...roject. [see more]

• Owner: Vikash Pandey

Allows users to either upload an image file or take a picture using their webcam and get a prediction the chemical structure depicted in the image in SMILES notation.

• Owner: Arnold Kochari

PML-RARA DB

• Owner: Xiangfu Zhong

This app allows users to input an image (in jpeg format) of a flower and get a prediction on what type of flower it is from a machine learning model. Top three most likely flower types according to the model’s prediction are shown.

• Owner: Arnold Kochari

peak cluster

• Owner: Vikash Pandey

In-silico Drug Repurposing Catalogue REMEDi4ALL (iDRC-R4A).

• Owner: Aleksandr Kushnir

Predicting chemical EC50 and EC10 ecotoxiticy values towards fish, aquatic invertebrate, and algae for a diverse set of effects using AI. Publication in Science Advances available through DOI: https://doi.org/10.1126/sciadv.adk6669

• Owner: Käll Styrbjörn

API for Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction. Refer to https://doi.org/10.3389/fphar.2018.01256 for the paper describing the tool.

• Owner: Hamza Saeed

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• Owner: Christophe Avenel

IFNB single-cell transcriptomics data

• Owner: Roy Francis

Trancriptom analysis for Suprcellfactories project

• Owner: Rasool Saghaleyni

scRNASeq of 55 samples from zebrafish brain. This project aims to characterize expression profile of different cell types.

• Owner: Nima Rafati

The Mouse Organ Metabolite Atlas

• Owner: Tomasz Czuba

Power analysis for RNA-Seq experiment. Estimate number of samples required and more.

• Owner: Roy Francis

Companion resource to the article, 'An online atlas of human plasma metabolite signatures of gut microbiome composition' by Dekkers et al

• Owner: Koen Dekkers

Meta-analysis of skeletal muscle response to exercise and inactivity

• Owner: Nicolas Pillon

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner: Lu Pan

Single Protein Localization

• Owner: Luay Aswad

Correlation Network

• Owner: Luay Aswad

Heatmap

• Owner: Luay Aswad

Network

• Owner: Luay Aswad

Data Download

• Owner: Luay Aswad

Application that allows users to get predictive data about compound (Multiple Molecules)

• Owner: Hamza Saeed

Application that allows users to get predictive data about compound (Single Molecule)

• Owner: Hamza Saeed

Imminent myocardial infarction prediction model. In patients free from prior cardiovascular disease, we aimed to identify characteristics of an imminent first heart attack and design a prediction model.

• Owner: Stefan Gustafsson

Shiny app for displaying Dictyostelium discoideum RNA-seq and proteomics data, from the publication Edelbroek et al. 2024

• Owner: Jakub Westholm

Model to predict the pKa of compounds

• Owner: Yojana Gadiya

All the browsable datasets from Lee et al 2024. "Open source, high throughput, targeted in situ transcriptomics"

• Owner: Marco Grillo

This dashboard visualises the spread of COVID-19 in Sweden: confirmed cases, ICU admissions, and deaths between February 2020 and March 2023.

• Owner: Arnold Kochari

Conformal regression model for predicting LogD for drug-like molecules, trained on ChEMBL version 33 with over 2.2M compounds using the CPSign software.

• Owner: Staffan Arvidsson McShane

Predicts Ames Mutagenicity for a chemical structure using an SVM model with Signatures features via the CPSign modeling tool.

• Owner: Ola Spjuth

RepurposeDrugs - an interactive web-based data portal and predictive platform for repurposing mono- and combination therapies.

• Owner: Aleksandr Kushnir

Modelling of cell-type signatures in the developmental human heart

• Owner: Christophe Avenel

Human heart development ISS datasets generated for Lazar et.al 2024.

• Owner: Sergio Marco Salas

Colorectal cancer usually metastasizes in the liver. Tumor cells can create two types of metastases: desmoplastic (DHGP) or replacement (RHGP). DHGP is characterized by a fibrotic rim that encapsulates the tumor cells and is associated with a better survival. In this project, we found two distinct areas in the rim: an outer area representing a ben...ign fibrotic reaction, and an inner area modified by the neighboring cancer cells. [see more]

• Owner: Axel Andersson

ALLIUM (ALL subtype Identification Using Machine learning) is a multimodal classifier of molecular subtypes in pediatric acute lymphoblastic leukemia, using DNA methylation (DNAm) and gene expression (GEX) data

• Owner: Mariya Lysenkova Wiklander

Demo of ROC curves, PR curves, and decision boundaries for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_roc

• Owner: Johan Henriksson

Demo of xgboost and decision trees for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_xgboost

• Owner: Johan Henriksson

API for model that predicts water–octanol distribution coefficient (logD) for chemical compounds: It is a proxy for the lipophilicity which is a major determinant of drug properties and overall suitability of drug candidates

• Owner: Hamza Saeed

A Shiny webapp for creating a Seurat object without programming expertise. Load a count matrix directory, interactively filter on metadata, view results, download Seurat object and results of differential gene expression testing.

• Owner: Rasmus Olofzon

Demo of penalized linear models (elastic net) for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_elasticnet

• Owner: Johan Henriksson

Demo of Bayesian linear models for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesianlinmod

• Owner: Johan Henriksson

Demo of markov chains and HMMs for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_markovchain

• Owner: Johan Henriksson

Demo of the Poisson distribution, as relevant for NGS, for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_poisson

• Owner: Johan Henriksson

Demo of statistical distributions for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_statdist

• Owner: Johan Henriksson

Co-occurrence plots created using VOS viewer . There are three plots in total, each based on publications from a different SciLifeLab reporting group (i.e. affiliated researchers, infrastructure units, and SciLifeLab fellows). In each plot, we have considered the KeyWords Plus associated with each paper.

• Owner: Senthilkumar Panneerselvam

An app to check color balance in indexes for sequencing

• Owner: Alma Hansen

Shiny app for exploration of the Genome-wide PeptidoGlycan Profiling dataset of Vibrio cholerae mutant library. Access to this app is password protected while it is under peer review.

• Owner: Laura Alvarez

The mappings are provided for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. This is a REST service for programmatic access to BridgeDb content, provided with interactive Swagger documentation using OpenAPI. For more info see https://www.bridgedb.org/.

• Owner: Arnold Kochari

Supplemental interactive visualization of Adipose Tissue Gene expression after exercise. Built using flexdashboard.

• Owner: Leonidas Lundell

A tool to predict the risk of experiencing refractory/relapse disease within two years in DLBCL patients treated with R-CHOP.

• Owner: Hui Wan

A single shiny solution from sequencer data to pathway analysis

• Owner: Jyotirmoy Das

This Shiny app is used the course CB2030 Systems biology at KTH Royal Instute of Technology.

• Owner: Thanadol Sutantiwanichkul

CellChat's Shiny app which allows interactive exploration of the cell-cell communication that are analyzed by the CellChat R-package

• Owner: Christophe Avenel

CoViMAPP (CoViD-19 Meta-Analysis of Plasma Proteins) is a meta-analysis resource of plasma proteins' alterations in COVID-19.

• Owner: Haris Babacic

OmicLoupe server. See https://quantitativeproteomics.org/omicloupe/ for info about OmicLoupe.

• Owner: Fredrik Levander

3D igraph from tsne with variable genes (Data from Tiklova et al. 2016)

• Owner: Nanjiang Shu

CitizenScience Project

• Owner: Nanjiang Shu

Single cell RNA sequencing dataset associated with the manuscript "Amnion signals are essential for mesoderm formation in primates"

• Owner: Nanjiang Shu

scRNA-seq data in: Small molecule screen identifies a salt-inducible kinase inhibitor inducing β-cell proliferation by transiently activating the unfolded protein response

• Owner: Nanjiang Shu

Byrnes, Lauren E., et al. Lineage dynamics of murine pancreatic development at single-cell resolution

• Owner: Nanjiang Shu

The Boreal Rhizospheric Atlas online tool was created to encourage exploration of a metatranscriptomic dataset of Norway spruce fine roots and their associated fungal communities from nutrient limited and nutrient enriched forest plots of the boreal region of Northern Sweden.

• Owner: Nicolas Delhomme